LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
# GJ thermostat

units   	metal
atom_style      full

boundary 	p p p
read_data argon.lmp
Reading data file ...
  orthogonal box = (0 0 0) to (32.146 32.146 32.146)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  864 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.007 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#

variable Ar equal 1

#############
#Atom Masses#
#############

mass ${Ar}      39.903
mass 1      39.903

###########################
#Pair Potentials - Tersoff#
###########################

pair_style      lj/cubic
pair_coeff      * * 0.0102701 3.42


velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin

timestep 0.1

compute myKE all ke
compute myPE all pe

fix lang all gjf 10 10 1 26488 vel vfull method 1

run 5000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- GJ methods: doi:10.1080/00268976.2019.1662506

@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}

- GJ-I vfull method: doi:10.1080/00268976.2012.760055

@Article{gronbech-jensen_simple_2013,
title = {A simple and effective Verlet-type algorithm for simulating Langevin dynamics},
volume = {111},
url = {http://www.tandfonline.com/doi/abs/10.1080/00268976.2012.760055},
doi = {10.1080/00268976.2012.760055},
pages = {983-991},
number = {8},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels and Farago, Oded},
year = {2013}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.9407173
  ghost atom cutoff = 6.9407173
  binsize = 3.4703587, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cubic, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   10            -56.207652      0             -55.092137      33.341103    
      5000   8.4535562     -55.150518      0             -54.207511      318.20862    
Loop time of 2.26831 on 1 procs for 5000 steps with 864 atoms

Performance: 19044.977 ns/day, 0.001 hours/ns, 2204.280 timesteps/s, 1.904 Matom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.2802     | 1.2802     | 1.2802     |   0.0 | 56.44
Bond    | 0.00051213 | 0.00051213 | 0.00051213 |   0.0 |  0.02
Neigh   | 0.27007    | 0.27007    | 0.27007    |   0.0 | 11.91
Comm    | 0.057527   | 0.057527   | 0.057527   |   0.0 |  2.54
Output  | 6.3876e-05 | 6.3876e-05 | 6.3876e-05 |   0.0 |  0.00
Modify  | 0.63364    | 0.63364    | 0.63364    |   0.0 | 27.93
Other   |            | 0.02635    |            |       |  1.16

Nlocal:            864 ave         864 max         864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1593 ave        1593 max        1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          18143 ave       18143 max       18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 258
Dangerous builds = 0

fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out

thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
      5000   8.4535562     -55.150518      0             -54.207511      318.20862    
      6000   8.4899401     -55.108242      0             -54.161176      331.10703    
      8000   8.3618893     -55.092171      0             -54.15939       334.11831    
     10000   8.8684311     -55.100316      0             -54.111029      334.09931    
     12000   8.4339192     -55.07343       0             -54.132614      340.00487    
     14000   8.072393      -55.115121      0             -54.214633      327.98965    
     16000   8.3420289     -55.077813      0             -54.147247      337.74926    
     18000   8.3803911     -55.12201       0             -54.187164      326.10485    
     20000   8.4676985     -55.176339      0             -54.231754      311.57092    
     22000   8.8560138     -55.110505      0             -54.122603      330.66179    
     24000   8.3187826     -55.120592      0             -54.192619      327.01148    
     26000   8.0327666     -55.116664      0             -54.220596      326.25179    
     28000   8.3672169     -55.130413      0             -54.197037      324.2368     
     30000   8.1669275     -55.057678      0             -54.146645      344.9168     
     32000   8.3819314     -55.08989       0             -54.154873      335.45317    
     34000   8.109088      -55.17222       0             -54.267639      310.83717    
     36000   8.3048574     -55.079475      0             -54.153056      338.04291    
     38000   8.8708544     -55.108991      0             -54.119434      330.70097    
     40000   8.4012779     -55.080817      0             -54.143642      338.54326    
Loop time of 18.9699 on 1 procs for 35000 steps with 864 atoms

Performance: 15941.040 ns/day, 0.002 hours/ns, 1845.028 timesteps/s, 1.594 Matom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 11.593     | 11.593     | 11.593     |   0.0 | 61.11
Bond    | 0.0041801  | 0.0041801  | 0.0041801  |   0.0 |  0.02
Neigh   | 2.2671     | 2.2671     | 2.2671     |   0.0 | 11.95
Comm    | 0.42339    | 0.42339    | 0.42339    |   0.0 |  2.23
Output  | 0.00062204 | 0.00062204 | 0.00062204 |   0.0 |  0.00
Modify  | 4.4976     | 4.4976     | 4.4976     |   0.0 | 23.71
Other   |            | 0.1839     |            |       |  0.97

Nlocal:            864 ave         864 max         864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1592 ave        1592 max        1592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          18144 ave       18144 max       18144 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 2122
Dangerous builds = 0
Total wall time: 0:00:21
